I would definitely pre-wash the flannel, regardless of whether or not the other fabric was pre-washed. Flannel tends to shrink a lot more than regular cotton does, and also sheds a lot of lint so I like to get as much of that off as possible so it doesn't all end up in my bobbin case. You might even want to wash it twice. (2nd wash can just be a quick rinse to get it wet, then toss in the dryer. The dryer is what does the shrinking.)
I don't see any reason you couldn't make the border out of flannel as well. I was actually going to do that on a quilt I'm working on now, but changed my mind. Not sure if I'd use flannel for the binding though - my gran did that a lot and it seems the flannel bindings wear out faster than regular cotton. Might have just been how the flannels were made in the 70's, though!